RE: Morpho - new version and dissertation publication

Fri, 15 Nov 2013 02:10:58 -0800


----- Forwarded message from "Lewis, Dr. Donald" <dle...@ksbhospital.com> -----

Date: Wed, 13 Nov 2013 10:46:17 -0500
From: "Lewis, Dr. Donald" <dle...@ksbhospital.com>
Reply-To: "Lewis, Dr. Donald" <dle...@ksbhospital.com>
Subject: RE: Morpho - new version and dissertation publication
To: morphmet@morphometrics.org

Stefan,
Congratulations on your achievement. I am an Otolaryngologist-Head and Neck Surgeon, and work with noses on a daily basis, outside of my paleoanthropology interests. I have downloaded your dissertation and look forward to reading it. Again, congratulations.
Don Lewis
-----Original Message-----
From: morphmet_modera...@morphometrics.org [mailto:morphmet_modera...@morphometrics.org]
Sent: Wednesday, November 13, 2013 12:45 AM
To: morphmet@morphometrics.org
Subject: Morpho - new version and dissertation publication


----- Forwarded message from Stefan Schlager <stefan.schla...@uniklinik-freiburg.de> -----

Date: Thu, 7 Nov 2013 06:37:42 -0500
From: Stefan Schlager <stefan.schla...@uniklinik-freiburg.de>
Reply-To: Stefan Schlager <stefan.schla...@uniklinik-freiburg.de>
Subject: Morpho - new version and dissertation publication
To: morphmet@morphometrics.org

Dear all,

I finally managed to release version 1.0 of my R-package Morpho with extended functionality and more examples.
I also managed to publish (online) my dissertationabout soft-tissue reconstruction of the human nose (including assessment population differences and sexual dimorphism) where some of the new features I included in this version (semi-automatic placement of semi-landmarks on multi-layer surface meshes) are explained.
It is available on: http://www.freidok.uni-freiburg.de/volltexte/9181/

Unfortunately for OS X users, the check on CRAN failed (only for OS X, probably caused by some issues in rgl). You can obtain the latest version via my sourcforge or github pages (http://sourceforge.net/projects/morpho-rpackage/ and https://github.com/zarquon42b/Morpho/releases). This version is even slightly newer than the one on CRAN. You will also need to install the latest version of "doParallel" and "rgl" beforehand.
All others can update with install.packages("Morpho")

I also invite the bold ones of you to use the latest snapshots that can be installed with devtools as described in the Wiki of Morphos Readme file

If you encounter bugs, please report them as  described in my FAQ (https://sourceforge.net/p/morpho-rpackage/wiki/FAQ/#q-how-can-i-report-a-bug)


Major new features:
  • placePatch: atlas based placement of semilandmarks on multiple meshes (including a variety of regularization routines to ensure that the correct surface is hit)
  • createAtlas, plotAtlas: creation and visualisation of an atlas needed in placePatch
  • checkLM: browse through a sample and check if landmarks are placed correctly
  • mergeMeshes: merge multiple triangular meshes into a single one
  • slider3d now allows the sliding on meshes already stored in the current workspace and has an option to prevent re-projection of fix landmarks onto the surface

Here is a list of all changes and bug fixes since 0.25-1:
  • added option "barycoords" in 'closemeshKD' and added normal weighting
  • made reprojection ind 'slider3d' using multiple cores in case "meshlist" is specified
  • added option "blockdiag" in 'CreateL' to supress returning blockdiagonal matrix containin Lsubk
  • significant speedup in calcGamma (responsible for sliding)
  • added option "meshlist" in 'slider3d' and fixed memory allocation problem for orthogonal projection with large amounts of landmarks in 'procSym' (underlying routine 'orp')
  • added autonaming of output in write.pts
  • 'mergeMeshes' now allows a list of meshes to merge
  • fixed error in 'mcNNindex' in case k=1
  • added landmark matrix to output of 'cExtract'
  • set pointsize to 10 in 'deformGrid3d' in case "type="p""
  • added options "silent"/"ignore.stdout" to 'ply2mesh', 'projRead', 'ray2mesh', 'slider3d' and 'warp.mesh' to supress terminal output
  • added option "pt.size" instead of "radius" in 'checkLM' and 'plotAtlas' to control point/sphere size.
  • added option "fixRepro" in 'slider3d' and 'relaxLM' to supress reprojection of fix landmarks onto the surface. This can be useful when some fix landmarks are in "thin air".
  • added support for point cloud export in 'mesh2ply' and 'mesh2obj'
  • added option "silent" in 'rmUnrefVertex'
  • fixed error in 'relWarps' preventing it to work for 2D configs
  • added function 'checkLM'. Useful to visualize if projection by 'placePatch' was successful by browsing through sample.
  • added functions 'placePatch', 'createAtlas' and 'plotAtlas' for defining templates and functions to project (semi-) landmarks from an atlas onto all specimen in a given sample
  • fixed missing '-1' subtraction in 'covW'
  • added function 'mergeMeshes' to concatenate multiple triangular meshes.
  • made function 'procAOVsym' (procrustes Anova for object symmetry) public.
  • made functions 'cSize', 'mcNNindex', 'meshcube', 'meshres', 'ProcGPA' public.
  • added option 'info' in 'read.mpp'
  • merged 'CreateL' and 'CreateL2D'
  • rewrote large parts of 'CVA', 'groupPCA' and 'permudist' to make the code more efficient
  • 'covPCA' now allows permutation tests to check if pairwise distances between covariance matrices are significant and reports rownames for two-group case
  • removed unnecessary complicated check for empty groups by simply using function 'factor' in 'covW' and 'typprobClass'
  • added option "mshape" to function 'orp' to specify a custom pole for projection
  • removed unnecessary sinus calculation in 'angle.calc'
All the best
Stefan
--
Dr. Stefan Schlager
Anthropologie
Medizinische Fakultät der der Albert Ludwigs- Universität Freiburg
Hebelstr. 29
79104 Freiburg

Anthropology
Faculty of Medicine, Albert-Ludwigs-University Freiburg
Hebelstr. 29
D- 79104 Freiburg

phone +49 (0)761 203-5522
fax +49 (0)761 203-6898



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